Hello.
I am trying to run AME from the MEME suite. I have tried to run it 2 times, 1st within the MEME suite, which has a option limited AME installation, and then outside of the MEME suite. What I am trying to do, is compare the level of enrichment of the JASPAR motifs in one file .fa using another .fa file as the background. I cannot seem to find a way within the MEME suite to not use partition mode and to explicitly define a positive file and a negative file, every time I try to set it so that there is no partition I get an error:
"Must set --fix-partition > 0"
if I try to set it so that the number of regions in the file is the same as the partition number, I just get the ame.txt file but without any results. (this is the case whether or not I assign a background file)
If I try to merge the background file and the positive region file (I am trying to do this analysis in two directions, 1st what motifs are enriched in the positive file and 2nd what motifs are enriched in the negative file), I get the same results for both as the algorithm seems to be taking the best N (partition number things) from the merged file.
So I tried the full AME algorithm downloaded from their site as a standalone program. When I try to run that with the same JASPAR_CORE.meme motif file it starts running:
"Using total hits scoring.
Using nucleotide alphabet (ACGTRYKMSWBDHVN).
Using background frequencies from NR sequence database."
but then I get this error:
"Reading motif MA0001.1FATAL: Can't find motif block in motif MA0001.1."
as soon as the program starts up.
Can anyone help me figure out what I am doing wrong, how to get AME to do this comparative analysis?
Thanks in advance!
I am trying to run AME from the MEME suite. I have tried to run it 2 times, 1st within the MEME suite, which has a option limited AME installation, and then outside of the MEME suite. What I am trying to do, is compare the level of enrichment of the JASPAR motifs in one file .fa using another .fa file as the background. I cannot seem to find a way within the MEME suite to not use partition mode and to explicitly define a positive file and a negative file, every time I try to set it so that there is no partition I get an error:
"Must set --fix-partition > 0"
if I try to set it so that the number of regions in the file is the same as the partition number, I just get the ame.txt file but without any results. (this is the case whether or not I assign a background file)
If I try to merge the background file and the positive region file (I am trying to do this analysis in two directions, 1st what motifs are enriched in the positive file and 2nd what motifs are enriched in the negative file), I get the same results for both as the algorithm seems to be taking the best N (partition number things) from the merged file.
So I tried the full AME algorithm downloaded from their site as a standalone program. When I try to run that with the same JASPAR_CORE.meme motif file it starts running:
"Using total hits scoring.
Using nucleotide alphabet (ACGTRYKMSWBDHVN).
Using background frequencies from NR sequence database."
but then I get this error:
"Reading motif MA0001.1FATAL: Can't find motif block in motif MA0001.1."
as soon as the program starts up.
Can anyone help me figure out what I am doing wrong, how to get AME to do this comparative analysis?
Thanks in advance!